When the shoguns consolidated power and took control of Japan in the early 1600s, foreigners were excluded throughout the country except for a Dutch trading post near Nagasaki. Along with that edict, Christianity was banned. At the time there were an estimated half a million Catholics in Japan, although for many individuals associating with the religion was of political and economic advantage rather than a true belief. Regardless, the shogunate feared the potential influence of the Christians in undermining their power as had happened in many other countries. The shogunate enforced the ban with brutality, including horrific torture and the massacre of thousands. Those whose faith was unshaken went far underground with their beliefs.

A little over two and a half centuries later, the shogunsí power had diminished and they were soon to be replaced with a return to the rule of the emperor backed by the nationalistic military. It is around this time that the historical novel Kikuís Prayer is set. The main character, Kiku, is a young maid who falls in love with Seikichi, a handsome peddler who lives in the next village near Nagasaki.

Because Nagasaki was the only Japanese city where foreigners were permitted, Christian ministers and priests were also allowed for the benefit of the foreigners posted there. In the novel, a young French Catholic priest, Bernard-Thadťe Petitjean, arrives in 1863 to take over from an older priest and to continue building the church his predecessor started. Petitjean is based on a real priest of the same name. Many other characters in the novel, both Japanese and foreign, are also based on historical figures. Petitjean arrives at his post with a personal missionóhe wants to find the Christians who have remained underground.

Petitjean takes daily walks asking if anyone knows of any Christians. Those he asks react in shock and deny that any Japanese Christians exist. The priest is naÔve about the severity of being a Japanese Christian, and to educate him, the old priest takes him to a boiling natural springs into which Christians who wouldnít renounce their faith were lowered until their flesh melted from their bones. Petitjean is distressed by this revelation, but canít entirely give up his search.

Kiku and Seikichi move toward marriage until she discovers he is one of the secretive Christians. She is dismayed because she doesnít understand why he would believe in the incomprehensible religion, one for which he would risk his life.

Petitjeanís daily walks attract the attention of the local officials, including the magistrate Ito who begins to keep tabs on the priest. And when Petitjean discovers a secret group of Christians, it isnít long before Ito and police detectives track them down and capture them. Seikichi is one of the captured.

Kiku is devastated and does all she can to find out what happened to him, even to the point of appealing to Petitjean. She doesnít understand how his God would allow his followers to be captured and tortured, some to death. As their imprisonment continues, Kiku, who is now working in the newly built church, implores to a statue of Mary to release Seikichi from his pain.

Seikichi and the others eventually denounce their faith and are released. But because they denounced their faith, they are ostracized from the other Christians when they return. Of course, Kiku is overjoyed that Seikichi is still alive. However, the Christians only renounced their faith to return to their village, and vow if caught again they would stay faithful to the bitter end.

When the shogunate falls and the Emperor returns to power, the Christians believe they will be free to practice their religion. However, the crackdowns continue, and they are rounded up again and taken to a prison far away, where torture is worse than before. Kiku moves to the region, and finds work in a brothel. There she does what she needs to do for money to give to Ito, who promises to bribe the prison officials to go easy on Seikichi. But Ito uses the money for his own pleasure, as he uses Kiku.

The ending of the novel is tragic and illuminating. By combining a fictional love story twisted by circumstances of historical events, Kikuís Prayer is a powerful and suspenseful read.